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- PDB-3fcx: Crystal structure of human esterase D -

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Basic information

Entry
Database: PDB / ID: 3fcx
TitleCrystal structure of human esterase D
ComponentsS-formylglutathione hydrolase
KeywordsHYDROLASE / retinoblastoma / genetic marker / esterase / Cytoplasm / Cytoplasmic vesicle / Polymorphism / Serine esterase
Function / homology
Function and homology information


S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / formaldehyde catabolic process / glutathione derivative biosynthetic process / Glutathione conjugation / carboxylic ester hydrolase activity / hydrolase activity, acting on ester bonds / cytoplasmic vesicle ...S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / methylumbelliferyl-acetate deacetylase / methylumbelliferyl-acetate deacetylase activity / formaldehyde catabolic process / glutathione derivative biosynthetic process / Glutathione conjugation / carboxylic ester hydrolase activity / hydrolase activity, acting on ester bonds / cytoplasmic vesicle / endoplasmic reticulum lumen / extracellular exosome / identical protein binding / cytosol
Similarity search - Function
S-formylglutathione hydrolase / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-formylglutathione hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWu, D. / Li, Y. / Song, G. / Zhang, D. / Shaw, N. / Liu, Z.J.
CitationJournal: Faseb J. / Year: 2009
Title: Crystal structure of human esterase D: a potential genetic marker of retinoblastoma
Authors: Wu, D. / Li, Y. / Song, G. / Zhang, D. / Shaw, N. / Liu, Z.J.
History
DepositionNov 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-formylglutathione hydrolase
B: S-formylglutathione hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2606
Polymers63,1162
Non-polymers1454
Water10,863603
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S-formylglutathione hydrolase
hetero molecules

A: S-formylglutathione hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2606
Polymers63,1162
Non-polymers1454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area1900 Å2
ΔGint-43.6 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.542, 70.724, 65.014
Angle α, β, γ (deg.)90.00, 108.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein S-formylglutathione hydrolase / / FGH / Esterase D


Mass: 31557.795 Da / Num. of mol.: 2 / Fragment: G257D
Source method: isolated from a genetically manipulated source
Details: Brain / Source: (gene. exp.) Homo sapiens (human) / Gene: ESD / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P10768, S-formylglutathione hydrolase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 603 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 30.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 200mm ammonium acetate, 30% PEG4000, pH5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2008 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 70703 / Num. obs: 69289 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.325 / Rsym value: 0.325 / Net I/σ(I): 20.5
Reflection shellHighest resolution: 1.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 20.5 / Num. unique all: 69289 / Rsym value: 0.325 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PV1

1pv1


Resolution: 1.5→40.16 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.924 / SU ML: 0.05 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.127 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19612 3500 5.1 %RANDOM
Rwork0.17581 ---
all0.1786 69289 --
obs0.17685 65767 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.953 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-0.26 Å2
2--0.73 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4293 0 4 603 4900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224381
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0321.9475939
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4895540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34224.433194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.19315696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4321510
X-RAY DIFFRACTIONr_chiral_restr0.0770.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213371
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6551.52701
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25324327
X-RAY DIFFRACTIONr_scbond_it2.41731680
X-RAY DIFFRACTIONr_scangle_it2.934.51611
X-RAY DIFFRACTIONr_rigid_bond_restr2.32534381
X-RAY DIFFRACTIONr_sphericity_free1.4313620
X-RAY DIFFRACTIONr_sphericity_bonded2.3634257
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 245 -
Rwork0.228 4782 -
obs--100 %

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